Started by user devspace Running as SYSTEM Building remotely on testintegration (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/BIOFORMATS-push The recommended git tool is: NONE No credentials specified > git rev-parse --resolve-git-dir /home/omero/workspace/BIOFORMATS-push/bio-formats-build/.git # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/ome/bio-formats-build # timeout=10 Cleaning workspace > git rev-parse --verify HEAD # timeout=10 Resetting working tree > git reset --hard # timeout=10 > git clean -ffdx # timeout=10 > git submodule foreach --recursive git reset --hard # timeout=10 > git submodule foreach --recursive git clean -fdx # timeout=10 Fetching upstream changes from https://github.com/ome/bio-formats-build > git --version # timeout=10 > git --version # 'git version 2.52.0' > git fetch --tags --force --progress -- https://github.com/ome/bio-formats-build +refs/heads/*:refs/remotes/origin/* # timeout=10 > git rev-parse origin/master^{commit} # timeout=10 Checking out Revision 5113234ae5277c95f7ebabe088d9441b2c5c1e7a (origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 5113234ae5277c95f7ebabe088d9441b2c5c1e7a # timeout=10 Commit message: "Merge pull request #732 from pwalczysko/deb-sec" > git rev-list --no-walk 5113234ae5277c95f7ebabe088d9441b2c5c1e7a # timeout=10 > git remote # timeout=10 > git submodule init # timeout=10 > git submodule sync # timeout=10 > git config --get remote.origin.url # timeout=10 > git submodule init # timeout=10 > git config -f .gitmodules --get-regexp ^submodule\.(.+)\.url # timeout=10 > git config --get submodule.ome-common-java.url # timeout=10 > git config -f .gitmodules --get submodule.ome-common-java.path # timeout=10 > git config --get submodule.ome-model.url # timeout=10 > git config -f .gitmodules --get submodule.ome-model.path # timeout=10 > git config --get submodule.ome-poi.url # timeout=10 > git config -f .gitmodules --get submodule.ome-poi.path # timeout=10 > git config --get submodule.ome-mdbtools.url # timeout=10 > git config -f .gitmodules --get submodule.ome-mdbtools.path # timeout=10 > git config --get submodule.ome-jai.url # timeout=10 > git config -f .gitmodules --get submodule.ome-jai.path # timeout=10 > git config --get submodule.ome-codecs.url # timeout=10 > git config -f .gitmodules --get submodule.ome-codecs.path # timeout=10 > git config --get submodule.ome-metakit.url # timeout=10 > git config -f .gitmodules --get submodule.ome-metakit.path # timeout=10 > git config --get submodule.ome-stubs.url # timeout=10 > git config -f .gitmodules --get submodule.ome-stubs.path # timeout=10 > git config --get submodule.bioformats.url # timeout=10 > git config -f .gitmodules --get submodule.bioformats.path # timeout=10 > git config --get submodule.bio-formats-documentation.url # timeout=10 > git config -f .gitmodules --get submodule.bio-formats-documentation.path # timeout=10 > git config --get submodule.bio-formats-examples.url # timeout=10 > git config -f .gitmodules --get submodule.bio-formats-examples.path # timeout=10 > git config --get submodule.ZarrReader.url # timeout=10 > git config -f .gitmodules --get submodule.ZarrReader.path # timeout=10 > git submodule update --init --recursive --remote ome-common-java # timeout=10 > git submodule update --init --recursive --remote ome-model # timeout=10 > git submodule update --init --recursive --remote ome-poi # timeout=10 > git submodule update --init --recursive --remote ome-mdbtools # timeout=10 > git submodule update --init --recursive --remote ome-jai # timeout=10 > git submodule update --init --recursive --remote ome-codecs # timeout=10 > git submodule update --init --recursive --remote ome-metakit # timeout=10 > git submodule update --init --recursive --remote ome-stubs # timeout=10 > git submodule update --init --recursive --remote bioformats # timeout=10 > git submodule update --init --recursive --remote bio-formats-documentation # timeout=10 > git submodule update --init --recursive --remote bio-formats-examples # timeout=10 > git submodule update --init --recursive --remote ZarrReader # timeout=10 [BIOFORMATS-push] $ /bin/bash -xe /tmp/jenkins2498426127558670858.sh + rm -rf /home/omero/workspace/BIOFORMATS-push/venv + python3.11 -m venv /home/omero/workspace/BIOFORMATS-push/venv + source /home/omero/workspace/BIOFORMATS-push/venv/bin/activate ++ deactivate nondestructive ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ '[' -n '' ']' ++ unset VIRTUAL_ENV ++ unset VIRTUAL_ENV_PROMPT ++ '[' '!' nondestructive = nondestructive ']' ++ VIRTUAL_ENV=/home/omero/workspace/BIOFORMATS-push/venv ++ export VIRTUAL_ENV ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ PATH=/home/omero/workspace/BIOFORMATS-push/venv/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ export PATH ++ '[' -n '' ']' ++ '[' -z '' ']' ++ _OLD_VIRTUAL_PS1= ++ PS1='(venv) ' ++ export PS1 ++ VIRTUAL_ENV_PROMPT='(venv) ' ++ export VIRTUAL_ENV_PROMPT ++ hash -r + python -m pip install 'pip @ https://files.pythonhosted.org/packages/3f/06/3e4420302363fbb71be3c7f35ce042f54bfca330e3e66b3a2e3c4cca579f/pip-26.2.2-py3-none-any.whl#sha256=fd7f4dfa8190e014013b9f08f3e973f4e4c26ffd179a204895533a7254813a70' Collecting pip@ https://files.pythonhosted.org/packages/3f/06/3e4420302363fbb71be3c7f35ce042f54bfca330e3e66b3a2e3c4cca579f/pip-26.2.2-py3-none-any.whl#sha256=fd7f4dfa8190e014013b9f08f3e973f4e4c26ffd179a204895533a7254813a70 Using cached pip-26.2.2-py3-none-any.whl (1.8 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 24.0 Uninstalling pip-24.0: Successfully uninstalled pip-24.0 Successfully installed pip-26.2.2 [notice] A new release of pip is available: 26.2.2 -> 26.3 [notice] To update, run: pip install --upgrade pip + python -m pip install --upgrade certifi Collecting certifi Downloading certifi-2026.10.23-py3-none-any.whl.metadata (2.5 kB) Downloading certifi-2026.10.23-py3-none-any.whl (135 kB) Installing collected packages: certifi Successfully installed certifi-2026.10.23 [notice] A new release of pip is available: 26.2.2 -> 26.3 [notice] To update, run: pip install --upgrade pip + echo '=== Python TLS environment ===' === Python TLS environment === + python --version Python 3.11.18 + python -m pip --version pip 26.2.2 from /home/omero/workspace/BIOFORMATS-push/venv/lib/python3.11/site-packages/pip (python 3.11) + python -c 'import certifi; print("certifi:", certifi.__version__); print("CA bundle:", certifi.where())' certifi: 2026.10.23 CA bundle: /home/omero/workspace/BIOFORMATS-push/venv/lib/python3.11/site-packages/certifi/cacert.pem ++ python -m certifi + CA=/home/omero/workspace/BIOFORMATS-push/venv/lib/python3.11/site-packages/certifi/cacert.pem + echo '=== Unwanted eMudhra roots ===' === Unwanted eMudhra roots === + grep -Eiq 'emSign ECC Root CA - G3|AAA Certificate Services' /home/omero/workspace/BIOFORMATS-push/venv/lib/python3.11/site-packages/certifi/cacert.pem + echo 'OK: neither unwanted root found' OK: neither unwanted root found + echo '=== eMudhra TLS rejection tests ===' === eMudhra TLS rejection tests === + python -m pip install --upgrade certifi requests Requirement already satisfied: certifi in ./venv/lib/python3.11/site-packages (2026.10.23) Collecting requests Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB) Collecting charset_normalizer<4,>=2 (from requests) Using cached charset_normalizer-3.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (46 kB) Collecting idna<4,>=2.5 (from requests) Using cached idna-3.20-py3-none-any.whl.metadata (7.2 kB) Collecting urllib3<3,>=1.26 (from requests) Downloading urllib3-2.8.0-py3-none-any.whl.metadata (7.4 kB) Using cached requests-2.34.2-py3-none-any.whl (73 kB) Using cached charset_normalizer-3.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (269 kB) Using cached idna-3.20-py3-none-any.whl (69 kB) Downloading urllib3-2.8.0-py3-none-any.whl (135 kB) Installing collected packages: urllib3, idna, charset_normalizer, requests Successfully installed charset_normalizer-3.5.2 idna-3.20 requests-2.34.2 urllib3-2.8.0 [notice] A new release of pip is available: 26.2.2 -> 26.3 [notice] To update, run: pip install --upgrade pip + python - PASS: dv-g3b-emudhra.we-have-a-problem.com rejected TLS (SSLError) PASS: dv-g3b-aaa-emudhra.we-have-a-problem.com rejected TLS (SSLError) + pip install -U scc Collecting scc Using cached scc-0.20.0-py3-none-any.whl.metadata (3.6 kB) Collecting PyGithub>=1.54 (from scc) Using cached pygithub-2.10.0-py3-none-any.whl.metadata (3.9 kB) Collecting PyYAML>=5.1 (from scc) Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB) Collecting future (from scc) Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB) Collecting ruamel.yaml (from scc) Using cached ruamel_yaml-0.19.1-py3-none-any.whl.metadata (16 kB) Collecting ruamel.yaml.jinja2 (from scc) Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl.metadata (2.9 kB) Collecting six (from scc) Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) Collecting urllib3<2 (from scc) Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) Collecting yaclifw<0.3,>=0.2.0 (from scc) Using cached yaclifw-0.2.0-py3-none-any.whl Collecting pynacl>=1.4.0 (from PyGithub>=1.54->scc) Using cached pynacl-1.6.2-cp38-abi3-manylinux_2_34_x86_64.whl.metadata (10.0 kB) Requirement already satisfied: requests>=2.14.0 in ./venv/lib/python3.11/site-packages (from PyGithub>=1.54->scc) (2.34.2) Collecting pyjwt>=2.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached pyjwt-2.15.1-py3-none-any.whl.metadata (3.5 kB) Collecting typing-extensions>=4.5.0 (from PyGithub>=1.54->scc) Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB) Collecting cryptography>=3.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached cryptography-50.0.2-cp311-abi3-manylinux_2_34_x86_64.whl.metadata (4.4 kB) Collecting cffi>=2.0.0 (from cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached cffi-2.1.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.5 kB) Collecting pycparser (from cffi>=2.0.0->cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Downloading pycparser-3.12-py3-none-any.whl.metadata (9.7 kB) Requirement already satisfied: charset_normalizer<4,>=2 in ./venv/lib/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.5.2) Requirement already satisfied: idna<4,>=2.5 in ./venv/lib/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.20) Requirement already satisfied: certifi>=2023.5.7 in ./venv/lib/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (2026.10.23) Using cached scc-0.20.0-py3-none-any.whl (48 kB) Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) Using cached pygithub-2.10.0-py3-none-any.whl (455 kB) Using cached pyjwt-2.15.1-py3-none-any.whl (33 kB) Using cached cryptography-50.0.2-cp311-abi3-manylinux_2_34_x86_64.whl (4.8 MB) Using cached cffi-2.1.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (217 kB) Using cached pynacl-1.6.2-cp38-abi3-manylinux_2_34_x86_64.whl (1.4 MB) Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB) Using cached typing_extensions-4.16.0-py3-none-any.whl (45 kB) Using cached future-1.0.0-py3-none-any.whl (491 kB) Downloading pycparser-3.12-py3-none-any.whl (62 kB) Using cached ruamel_yaml-0.19.1-py3-none-any.whl (118 kB) Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl (5.5 kB) Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) Installing collected packages: urllib3, typing-extensions, six, ruamel.yaml, PyYAML, pyjwt, pycparser, future, yaclifw, ruamel.yaml.jinja2, cffi, pynacl, cryptography, PyGithub, scc Attempting uninstall: urllib3 Found existing installation: urllib3 2.8.0 Uninstalling urllib3-2.8.0: Successfully uninstalled urllib3-2.8.0 Successfully installed PyGithub-2.10.0 PyYAML-6.0.3 cffi-2.1.1 cryptography-50.0.2 future-1.0.0 pycparser-3.12 pyjwt-2.15.1 pynacl-1.6.2 ruamel.yaml-0.19.1 ruamel.yaml.jinja2-0.2.7 scc-0.20.0 six-1.17.0 typing-extensions-4.16.0 urllib3-1.26.20 yaclifw-0.2.0 [notice] A new release of pip is available: 26.2.2 -> 26.3 [notice] To update, run: pip install --upgrade pip + PATH=/home/omero/workspace/BIOFORMATS-push/bio-formats-build/scripts:/home/omero/workspace/BIOFORMATS-push/venv/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin + MERGE_OPTIONS='--no-ask --reset --comment -S success-only' + cd bio-formats-build + echo '=== Git remote protocols ===' === Git remote protocols === + git remote -v origin https://github.com/ome/bio-formats-build (fetch) origin https://github.com/ome/bio-formats-build (push) + git submodule foreach --recursive 'echo "$name"; git remote -v' Entering 'ZarrReader' ZarrReader origin https://github.com/ome/ZarrReader.git (fetch) origin https://github.com/ome/ZarrReader.git (push) Entering 'bio-formats-documentation' bio-formats-documentation origin https://github.com/ome/bio-formats-documentation.git (fetch) origin https://github.com/ome/bio-formats-documentation.git (push) Entering 'bio-formats-examples' bio-formats-examples origin https://github.com/ome/bio-formats-examples.git (fetch) origin https://github.com/ome/bio-formats-examples.git (push) Entering 'bioformats' bioformats origin https://github.com/openmicroscopy/bioformats.git (fetch) origin https://github.com/openmicroscopy/bioformats.git (push) Entering 'ome-codecs' ome-codecs origin https://github.com/ome/ome-codecs.git (fetch) origin https://github.com/ome/ome-codecs.git (push) Entering 'ome-common-java' ome-common-java origin https://github.com/ome/ome-common-java.git (fetch) origin https://github.com/ome/ome-common-java.git (push) Entering 'ome-jai' ome-jai origin https://github.com/ome/ome-jai.git (fetch) origin https://github.com/ome/ome-jai.git (push) Entering 'ome-mdbtools' ome-mdbtools origin https://github.com/ome/ome-mdbtools.git (fetch) origin https://github.com/ome/ome-mdbtools.git (push) Entering 'ome-metakit' ome-metakit origin https://github.com/ome/ome-metakit.git (fetch) origin https://github.com/ome/ome-metakit.git (push) Entering 'ome-model' ome-model origin https://github.com/ome/ome-model.git (fetch) origin https://github.com/ome/ome-model.git (push) Entering 'ome-poi' ome-poi origin https://github.com/ome/ome-poi.git (fetch) origin https://github.com/ome/ome-poi.git (push) Entering 'ome-stubs' ome-stubs origin https://github.com/ome/ome-stubs.git (fetch) origin https://github.com/ome/ome-stubs.git (push) + echo 'Merge base repository (no submodule updates)' Merge base repository (no submodule updates) + scc merge --no-ask --reset --comment -S success-only --shallow master 2026-11-09 13:37:25,246 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-11-09 13:37:25,246 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-11-09 13:37:25,246 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-11-09 13:37:25,246 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-11-09 13:37:25,247 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-11-09 13:37:25,247 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2026-11-09 13:37:35,187 [ scc.merge] INFO Repository: ome/bio-formats-build 2026-11-09 13:37:35,187 [ scc.merge] INFO Already up to date. 2026-11-09 13:37:35,187 [ scc.merge] INFO 2026-11-09 13:37:35,187 [ scc.merge] INFO Merged PRs: 2026-11-09 13:37:35,187 [ scc.merge] INFO - PR 735 pwalczysko 'Patch 1 continue' 2026-11-09 13:37:35,187 [ scc.merge] INFO + git submodule sync Synchronizing submodule url for 'ZarrReader' Synchronizing submodule url for 'bio-formats-documentation' Synchronizing submodule url for 'bio-formats-examples' Synchronizing submodule url for 'bioformats' Synchronizing submodule url for 'ome-codecs' Synchronizing submodule url for 'ome-common-java' Synchronizing submodule url for 'ome-jai' Synchronizing submodule url for 'ome-mdbtools' Synchronizing submodule url for 'ome-metakit' Synchronizing submodule url for 'ome-model' Synchronizing submodule url for 'ome-poi' Synchronizing submodule url for 'ome-stubs' + git submodule update --remote --recursive Submodule path 'ZarrReader': checked out '5f3faa45fef73473bce6e4fc732a9cccc05c105d' Submodule path 'bio-formats-documentation': checked out '43e3ed971f94ea85da5dd9fdc92349e7b452bdf8' Submodule path 'bio-formats-examples': checked out 'd92cafefa7c3bd86bddba0f1e6d85ed71aa58645' Submodule path 'bioformats': checked out '6c69b36f0da06065b008632a467828b29b7d49bb' Submodule path 'ome-codecs': checked out '61a7334fea6533ba945c2279a6d62a216a365936' Submodule path 'ome-common-java': checked out 'a704a2abe26d165bc53bd5cd0da5a5c464f53987' Submodule path 'ome-jai': checked out '029d825eea01e9d5f3c12528a230c95cd71a0cd1' Submodule path 'ome-mdbtools': checked out '52241813f78efa5191175a7952c0b2d89c215498' Submodule path 'ome-metakit': checked out 'b953d0b0b8b7eabae84e98c262f2ac7049ffb92a' Submodule path 'ome-model': checked out 'b709663ad411da68e4330da6a7d6fb105e9eec31' Submodule path 'ome-poi': checked out 'f179bf4f5fcc0499d065a0e0b40141a2834e1751' Submodule path 'ome-stubs': checked out '5a2fdd0aa37fef5d34942d367f57de6f5916fc06' + echo 'Merge all submodules using repository configuration:' Merge all submodules using repository configuration: + cat scripts/repositories.yml base-branch: master submodules: ome-common-java: base-branch: master bioformats: base-branch: develop bio-formats-documentation: base-branch: master bio-formats-examples: base-branch: master ome-codecs: base-branch: master ome-common-java: base-branch: master ome-jai: base-branch: master ome-mdbtools: base-branch: master ome-metakit: base-branch: master ome-model: base-branch: master ome-poi: base-branch: master ome-stubs: base-branch: master ZarrReader: base-branch: main ++ pwd + scc merge --repository-config=/home/omero/workspace/BIOFORMATS-push/bio-formats-build/scripts/repositories.yml --no-ask --reset --comment -S success-only --update-gitmodules --push merge_ci master Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503 2026-11-09 13:38:03,025 [github.Reque] INFO Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503 2026-11-09 13:38:36,473 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-11-09 13:38:36,473 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-11-09 13:38:36,473 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-11-09 13:38:36,474 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-11-09 13:38:36,474 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-11-09 13:38:36,474 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2026-11-09 13:38:42,060 [ scc.git] INFO Overriding base-branch from master to main 2026-11-09 13:39:43,736 [ scc.git] INFO Overriding base-branch from master to develop 2026-11-09 13:40:19,697 [ scc.git] ERROR stderr (git merge --ff-only origin/develop): Updating files: 56% (104/184) Updating files: 57% (105/184) Updating files: 58% (107/184) Updating files: 59% (109/184) Updating files: 60% (111/184) Updating files: 61% (113/184) Updating 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114 dominikl 'Archive ZarrReader' 2026-11-09 13:42:48,188 [ scc.merge] INFO 2026-11-09 13:42:48,188 [ scc.merge] INFO Repository: ome/bio-formats-documentation 2026-11-09 13:42:48,188 [ scc.merge] INFO Updating db99c10d..43e3ed97 2026-11-09 13:42:48,188 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,188 [ scc.merge] INFO - PR 494 melissalinkert 'Update command line options for `showinf` and `bfconvert`' 2026-11-09 13:42:48,188 [ scc.merge] INFO - PR 493 pwalczysko 'Replace http with https and go directly to miltenyi' 2026-11-09 13:42:48,188 [ scc.merge] INFO - PR 489 pwalczysko 'Ignore web.archive.org 429' 2026-11-09 13:42:48,188 [ scc.merge] INFO - PR 492 melissalinkert 'Remove references to `ZarrReader`' 2026-11-09 13:42:48,188 [ scc.merge] INFO - PR 491 melissalinkert 'Build cleanup' 2026-11-09 13:42:48,188 [ scc.merge] INFO - PR 487 pwalczysko 'Gatan2' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 484 pwalczysko 'Ignore loc.gov because of captcha' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 483 melissalinkert 'Add section on deprecated API' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 476 melissalinkert 'Update logback to 1.5.37' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 477 melissalinkert 'Replace Olympus SIS link' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 471 dominikl 'Replace faqs.org links' 2026-11-09 13:42:48,189 [ scc.merge] INFO - PR 474 dominikl 'exclude unidata' 2026-11-09 13:42:48,190 [ scc.merge] INFO - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' 2026-11-09 13:42:48,190 [ scc.merge] INFO - PR 472 dominikl 'ignore nih.gov' 2026-11-09 13:42:48,190 [ scc.merge] INFO - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 2026-11-09 13:42:48,190 [ scc.merge] INFO - PR 469 sbesson 'Update Unidata releases URL' 2026-11-09 13:42:48,190 [ scc.merge] INFO - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' 2026-11-09 13:42:48,190 [ scc.merge] INFO - PR 465 pwalczysko 'Ignore umassmed.edu, 403' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 463 pwalczysko 'Ignore zenodo 403' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 461 melissalinkert 'Release notes for 8.5.0' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 458 pwalczysko 'Konica olympus' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 455 melissalinkert 'Add TFCYTO page' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 454 melissalinkert 'Release notes for 8.4.0' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 453 pwalczysko 'Fix links' 2026-11-09 13:42:48,191 [ scc.merge] INFO - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 450 melissalinkert 'Update a couple of outdated lines in about page' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 445 melissalinkert 'Update ome-common to 6.1.1' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 442 will-moore 'Link to Receipt of Sample Data' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 441 melissalinkert 'Update external readers page based upon feedback' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 439 melissalinkert 'Start describing external reader usage' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 438 will-moore 'Fix netcdf-java links' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 437 pwalczysko 'Nis elements and cibc-datasets' 2026-11-09 13:42:48,192 [ scc.merge] INFO - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' 2026-11-09 13:42:48,193 [ scc.merge] INFO - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' 2026-11-09 13:42:48,193 [ scc.merge] INFO - PR 434 sbesson 'Add format page for Zeiss XRM format' 2026-11-09 13:42:48,193 [ scc.merge] INFO - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' 2026-11-09 13:42:48,193 [ scc.merge] INFO - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' 2026-11-09 13:42:48,193 [ scc.merge] INFO - PR 431 pwalczysko 'Fix limited javadoc syntax' 2026-11-09 13:42:48,193 [ scc.merge] INFO - PR 430 pwalczysko 'Fix sourceforge' 2026-11-09 13:42:48,193 [ scc.merge] INFO - PR 426 jburel 'Update EMAN2 URL' 2026-11-09 13:42:48,194 [ scc.merge] INFO - PR 427 jburel 'Checking linkcheck config' 2026-11-09 13:42:48,194 [ scc.merge] INFO - PR 422 melissalinkert 'Add page for JDCE' 2026-11-09 13:42:48,196 [ scc.merge] INFO - PR 425 melissalinkert 'Release notes for 8.2.0' 2026-11-09 13:42:48,196 [ scc.merge] INFO - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' 2026-11-09 13:42:48,196 [ scc.merge] INFO - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' 2026-11-09 13:42:48,196 [ scc.merge] INFO - PR 418 sbesson 'Update MATLAB documentation for colormap return value' 2026-11-09 13:42:48,197 [ scc.merge] INFO - PR 421 dominikl 'Exclude merckmillipore.com from link check' 2026-11-09 13:42:48,197 [ scc.merge] INFO 2026-11-09 13:42:48,197 [ scc.merge] INFO Merged PRs: 2026-11-09 13:42:48,197 [ scc.merge] INFO - PR 481 melissalinkert 'Remove dependencies associated with minio, jackson, and guava' 2026-11-09 13:42:48,197 [ scc.merge] INFO - PR 495 melissalinkert 'Document new axis orientation API' 2026-11-09 13:42:48,197 [ scc.merge] INFO 2026-11-09 13:42:48,198 [ scc.merge] INFO Repository: ome/bio-formats-examples 2026-11-09 13:42:48,198 [ scc.merge] INFO Updating 3aa7013..d92cafe 2026-11-09 13:42:48,198 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,198 [ scc.merge] INFO - PR 143 sbesson 'Build upgrades' 2026-11-09 13:42:48,198 [ scc.merge] INFO - PR 139 melissalinkert 'Fix markers for tile conversion example' 2026-11-09 13:42:48,198 [ scc.merge] INFO - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' 2026-11-09 13:42:48,199 [ scc.merge] INFO - PR 136 melissalinkert 'Add precompressed tile writing example' 2026-11-09 13:42:48,199 [ scc.merge] INFO - PR 137 melissalinkert 'Fix output path for in-memory writing test' 2026-11-09 13:42:48,199 [ scc.merge] INFO - PR 135 melissalinkert 'Bump logback version to 1.3.16' 2026-11-09 13:42:48,199 [ scc.merge] INFO - PR 134 sbesson 'POM: cleanup outdated metadata' 2026-11-09 13:42:48,199 [ scc.merge] INFO 2026-11-09 13:42:48,199 [ scc.merge] INFO 2026-11-09 13:42:48,200 [ scc.merge] INFO Repository: openmicroscopy/bioformats 2026-11-09 13:42:48,200 [ scc.merge] INFO Excluded PRs: 2026-11-09 13:42:48,200 [ scc.merge] INFO - PR 4498 salehtahini 'Updated ImspectorReader.java' (user: salehtahini) 2026-11-09 13:42:48,200 [ scc.merge] INFO - PR 4490 mkitti 'Switch from cisd:jhdf5 to janelia-jhdf5' (stage: draft) 2026-11-09 13:42:48,200 [ scc.merge] INFO - PR 4488 LMS-MichaelGoelzer 'Leica channel names' (user: LMS-MichaelGoelzer) 2026-11-09 13:42:48,200 [ scc.merge] INFO - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) 2026-11-09 13:42:48,201 [ scc.merge] INFO - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) 2026-11-09 13:42:48,201 [ scc.merge] INFO - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) 2026-11-09 13:42:48,201 [ scc.merge] INFO - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) 2026-11-09 13:42:48,201 [ scc.merge] INFO - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) 2026-11-09 13:42:48,201 [ scc.merge] INFO Updating 3f70394503..6c69b36f0d 2026-11-09 13:42:48,201 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,201 [ scc.merge] INFO - PR 4497 melissalinkert 'Switch to https://central.sonatype.com/artifact/com.glencoesoftware/libjpeg-turbo/0.1.0' 2026-11-09 13:42:48,202 [ scc.merge] INFO - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' 2026-11-09 13:42:48,202 [ scc.merge] INFO - PR 4496 melissalinkert 'Expand memo usage test to cover reopening when only the file was closed' 2026-11-09 13:42:48,202 [ scc.merge] INFO - PR 4489 melissalinkert 'OME-TIFF: remove extra Channels all at once' 2026-11-09 13:42:48,202 [ scc.merge] INFO - PR 4491 melissalinkert 'Remove `ZarrReader` from `readers.txt`' 2026-11-09 13:42:48,202 [ scc.merge] INFO - PR 4485 melissalinkert 'Operetta: normalize file separators' 2026-11-09 13:42:48,202 [ scc.merge] INFO - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' 2026-11-09 13:42:48,202 [ scc.merge] INFO - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' 2026-11-09 13:42:48,202 [ scc.merge] INFO - PR 4486 melissalinkert 'Upgrade check cleanup' 2026-11-09 13:42:48,203 [ scc.merge] INFO - PR 4479 melissalinkert 'Physical sizes for subresolutions' 2026-11-09 13:42:48,203 [ scc.merge] INFO - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' 2026-11-09 13:42:48,203 [ scc.merge] INFO - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' 2026-11-09 13:42:48,203 [ scc.merge] INFO - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' 2026-11-09 13:42:48,203 [ scc.merge] INFO - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' 2026-11-09 13:42:48,203 [ scc.merge] INFO - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' 2026-11-09 13:42:48,203 [ scc.merge] INFO - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' 2026-11-09 13:42:48,204 [ scc.merge] INFO - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' 2026-11-09 13:42:48,204 [ scc.merge] INFO - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' 2026-11-09 13:42:48,204 [ scc.merge] INFO - PR 4445 melissalinkert '.vsi fill color fixes' 2026-11-09 13:42:48,204 [ scc.merge] INFO - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' 2026-11-09 13:42:48,204 [ scc.merge] INFO - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' 2026-11-09 13:42:48,204 [ scc.merge] INFO - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' 2026-11-09 13:42:48,204 [ scc.merge] INFO - PR 4452 melissalinkert 'Update logback to 1.5.37' 2026-11-09 13:42:48,205 [ scc.merge] INFO - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' 2026-11-09 13:42:48,205 [ scc.merge] INFO - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' 2026-11-09 13:42:48,205 [ scc.merge] INFO - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' 2026-11-09 13:42:48,205 [ scc.merge] INFO - PR 4438 melissalinkert 'Remove unnecessary negative checks' 2026-11-09 13:42:48,205 [ scc.merge] INFO - PR 4436 melissalinkert 'xmlvalid cleanup' 2026-11-09 13:42:48,206 [ scc.merge] INFO - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-11-09 13:42:48,206 [ scc.merge] INFO - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' 2026-11-09 13:42:48,206 [ scc.merge] INFO - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' 2026-11-09 13:42:48,206 [ scc.merge] INFO - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' 2026-11-09 13:42:48,206 [ scc.merge] INFO - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' 2026-11-09 13:42:48,206 [ scc.merge] INFO - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' 2026-11-09 13:42:48,206 [ scc.merge] INFO - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' 2026-11-09 13:42:48,206 [ scc.merge] INFO - PR 4419 melissalinkert 'Update to ome-common 6.2.1' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4417 melissalinkert 'VSI: recognize calibration function tag' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4406 sbesson 'Fix Javadoc warnings' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' 2026-11-09 13:42:48,207 [ scc.merge] INFO - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' 2026-11-09 13:42:48,208 [ scc.merge] INFO - PR 4392 melissalinkert 'A few more ND2 dimension fixes' 2026-11-09 13:42:48,208 [ scc.merge] INFO - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' 2026-11-09 13:42:48,208 [ scc.merge] INFO - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' 2026-11-09 13:42:48,208 [ scc.merge] INFO - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' 2026-11-09 13:42:48,208 [ scc.merge] INFO - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' 2026-11-09 13:42:48,208 [ scc.merge] INFO - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' 2026-11-09 13:42:48,208 [ scc.merge] INFO - PR 4388 melissalinkert 'Update to CodeQL v4' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4384 melissalinkert 'Update ome-common to 6.1.1' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4383 melissalinkert 'Bump logback version to 1.3.16' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4374 melissalinkert 'CellH5: reduce memory usage' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4360 melissalinkert 'Fix several OIR issues' 2026-11-09 13:42:48,209 [ scc.merge] INFO - PR 4365 melissalinkert 'Fix array sizes in Octave' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4361 melissalinkert 'Remove unused detector linking logic' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4353 melissalinkert 'Fix tag encoding for LEO files' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4348 sbesson 'FakeReader: link instrument to all images' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' 2026-11-09 13:42:48,210 [ scc.merge] INFO - PR 4307 jburel 'Build report' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4338 sbesson 'org.openmicroscopy component updates' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' 2026-11-09 13:42:48,211 [ scc.merge] INFO - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4327 melissalinkert 'Check modulo values in repository tests' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4284 ptahmose 'fix for garbled images with CZIs' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' 2026-11-09 13:42:48,212 [ scc.merge] INFO - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' 2026-11-09 13:42:48,213 [ scc.merge] INFO - PR 4303 melissalinkert 'Fix Unidata repository URLs' 2026-11-09 13:42:48,213 [ scc.merge] INFO 2026-11-09 13:42:48,213 [ scc.merge] INFO Merged PRs: 2026-11-09 13:42:48,213 [ scc.merge] INFO - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' 2026-11-09 13:42:48,213 [ scc.merge] INFO - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' 2026-11-09 13:42:48,213 [ scc.merge] INFO - PR 4362 ngladitz 'OBF: Support complex data stacks' 2026-11-09 13:42:48,213 [ scc.merge] INFO - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' 2026-11-09 13:42:48,213 [ scc.merge] INFO - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' 2026-11-09 13:42:48,213 [ scc.merge] INFO - PR 4499 melissalinkert 'Remove guava dependency' 2026-11-09 13:42:48,213 [ scc.merge] INFO 2026-11-09 13:42:48,213 [ scc.merge] INFO Repository: ome/ome-codecs 2026-11-09 13:42:48,213 [ scc.merge] INFO Updating fab1a01..61a7334 2026-11-09 13:42:48,213 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,213 [ scc.merge] INFO - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-11-09 13:42:48,213 [ scc.merge] INFO - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' 2026-11-09 13:42:48,215 [ scc.merge] INFO - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' 2026-11-09 13:42:48,215 [ scc.merge] INFO - PR 43 melissalinkert 'Update to ome-common 6.1.1' 2026-11-09 13:42:48,216 [ scc.merge] INFO - PR 42 sbesson 'Update publication build system to use Central Portal' 2026-11-09 13:42:48,216 [ scc.merge] INFO 2026-11-09 13:42:48,216 [ scc.merge] INFO 2026-11-09 13:42:48,216 [ scc.merge] INFO Repository: ome/ome-common-java 2026-11-09 13:42:48,216 [ scc.merge] INFO Updating 2cb0b7b..a704a2a 2026-11-09 13:42:48,216 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,216 [ scc.merge] INFO - PR 108 dominikl 'Remove S3 handling' 2026-11-09 13:42:48,217 [ scc.merge] INFO - PR 117 melissalinkert 'Update logback to 1.5.37' 2026-11-09 13:42:48,217 [ scc.merge] INFO - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' 2026-11-09 13:42:48,218 [ scc.merge] INFO - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-11-09 13:42:48,218 [ scc.merge] INFO - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' 2026-11-09 13:42:48,218 [ scc.merge] INFO - PR 112 melissalinkert 'Standardize XML parsing' 2026-11-09 13:42:48,218 [ scc.merge] INFO - PR 111 sbesson 'XMLTools: use try-with-resources statement' 2026-11-09 13:42:48,218 [ scc.merge] INFO - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' 2026-11-09 13:42:48,219 [ scc.merge] INFO - PR 107 sbesson 'Add GitHub release creation to Maven workflow' 2026-11-09 13:42:48,219 [ scc.merge] INFO - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' 2026-11-09 13:42:48,219 [ scc.merge] INFO - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' 2026-11-09 13:42:48,219 [ scc.merge] INFO - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' 2026-11-09 13:42:48,220 [ scc.merge] INFO - PR 99 melissalinkert 'Fix type of skipped bytes counter' 2026-11-09 13:42:48,220 [ scc.merge] INFO - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' 2026-11-09 13:42:48,220 [ scc.merge] INFO 2026-11-09 13:42:48,220 [ scc.merge] INFO Merged PRs: 2026-11-09 13:42:48,220 [ scc.merge] INFO - PR 121 melissalinkert 'Remove guava dependency' 2026-11-09 13:42:48,220 [ scc.merge] INFO 2026-11-09 13:42:48,220 [ scc.merge] INFO Repository: ome/ome-jai 2026-11-09 13:42:48,220 [ scc.merge] INFO Updating e70c2ab..029d825 2026-11-09 13:42:48,220 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,220 [ scc.merge] INFO - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-11-09 13:42:48,220 [ scc.merge] INFO - PR 8 sbesson 'Update publication build system to use Central Portal ' 2026-11-09 13:42:48,220 [ scc.merge] INFO - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' 2026-11-09 13:42:48,220 [ scc.merge] INFO 2026-11-09 13:42:48,220 [ scc.merge] INFO 2026-11-09 13:42:48,220 [ scc.merge] INFO Repository: ome/ome-mdbtools 2026-11-09 13:42:48,220 [ scc.merge] INFO Updating 9193930..5224181 2026-11-09 13:42:48,220 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,220 [ scc.merge] INFO - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-11-09 13:42:48,220 [ scc.merge] INFO - PR 14 sbesson 'Update publication system to use Central Portal' 2026-11-09 13:42:48,220 [ scc.merge] INFO 2026-11-09 13:42:48,220 [ scc.merge] INFO 2026-11-09 13:42:48,221 [ scc.merge] INFO Repository: ome/ome-metakit 2026-11-09 13:42:48,221 [ scc.merge] INFO Updating 1ba6cf1..b953d0b 2026-11-09 13:42:48,221 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 34 melissalinkert 'Update logback to 1.5.37' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 30 melissalinkert 'Update ome-common to 6.1.1' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 27 sbesson 'Update publication build system to use Central Portal' 2026-11-09 13:42:48,221 [ scc.merge] INFO 2026-11-09 13:42:48,221 [ scc.merge] INFO 2026-11-09 13:42:48,221 [ scc.merge] INFO Repository: ome/ome-model 2026-11-09 13:42:48,221 [ scc.merge] INFO Updating 3d70a1f9..b709663a 2026-11-09 13:42:48,221 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 232 melissalinkert 'Update logback to 1.5.37' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' 2026-11-09 13:42:48,221 [ scc.merge] INFO - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' 2026-11-09 13:42:48,222 [ scc.merge] INFO - PR 225 melissalinkert 'Update ome-common to 6.1.1' 2026-11-09 13:42:48,222 [ scc.merge] INFO - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' 2026-11-09 13:42:48,222 [ scc.merge] INFO - PR 224 sbesson 'Add release step to GitHub Maven workflow' 2026-11-09 13:42:48,223 [ scc.merge] INFO - PR 222 sbesson 'Update publication build system to use Central Portal' 2026-11-09 13:42:48,223 [ scc.merge] INFO - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' 2026-11-09 13:42:48,223 [ scc.merge] INFO 2026-11-09 13:42:48,223 [ scc.merge] INFO 2026-11-09 13:42:48,224 [ scc.merge] INFO Repository: ome/ome-poi 2026-11-09 13:42:48,224 [ scc.merge] INFO Updating da3a5f3..f179bf4 2026-11-09 13:42:48,224 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,224 [ scc.merge] INFO - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-11-09 13:42:48,225 [ scc.merge] INFO - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' 2026-11-09 13:42:48,225 [ scc.merge] INFO - PR 20 melissalinkert 'Update to ome-common 6.1.1' 2026-11-09 13:42:48,225 [ scc.merge] INFO - PR 19 sbesson 'Update publication system to use Central Portal' 2026-11-09 13:42:48,225 [ scc.merge] INFO 2026-11-09 13:42:48,225 [ scc.merge] INFO 2026-11-09 13:42:48,225 [ scc.merge] INFO Repository: ome/ome-stubs 2026-11-09 13:42:48,225 [ scc.merge] INFO Updating 1559997..5a2fdd0 2026-11-09 13:42:48,225 [ scc.merge] INFO Previously merged: 2026-11-09 13:42:48,225 [ scc.merge] INFO - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-11-09 13:42:48,225 [ scc.merge] INFO - PR 12 sbesson 'Update publication build system to use Central Portal' 2026-11-09 13:42:48,225 [ scc.merge] INFO 2026-11-09 13:42:48,225 [ scc.merge] INFO Merged PRs: 2026-11-09 13:42:48,225 [ scc.merge] INFO - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' 2026-11-09 13:42:48,225 [ scc.merge] INFO 2026-11-09 13:43:29,757 [ scc.merge] INFO Merged branch pushed to https://github.com/snoopycrimecop/bio-formats-build/tree/merge_ci + echo 'Update maven component versions' Update maven component versions + echo 'Commit all component version changes' Commit all component version changes + git submodule foreach 'git add -u' Entering 'ZarrReader' Entering 'bio-formats-documentation' Entering 'bio-formats-examples' Entering 'bioformats' Entering 'ome-codecs' Entering 'ome-common-java' Entering 'ome-jai' Entering 'ome-mdbtools' Entering 'ome-metakit' Entering 'ome-model' Entering 'ome-poi' Entering 'ome-stubs' + git submodule foreach 'git commit -m '\''Update component versions'\'' || true' Entering 'ZarrReader' HEAD detached from 31d6d95 nothing to commit, working tree clean Entering 'bio-formats-documentation' HEAD detached from db99c10d nothing to commit, working tree clean Entering 'bio-formats-examples' HEAD detached from 3aa7013 nothing to commit, working tree clean Entering 'bioformats' HEAD detached from 3f70394503 nothing to commit, working tree clean Entering 'ome-codecs' HEAD detached from fab1a01 nothing to commit, working tree clean Entering 'ome-common-java' HEAD detached from 2cb0b7b nothing to commit, working tree clean Entering 'ome-jai' HEAD detached from e70c2ab nothing to commit, working tree clean Entering 'ome-mdbtools' HEAD detached from 9193930 nothing to commit, working tree clean Entering 'ome-metakit' HEAD detached from 1ba6cf1 nothing to commit, working tree clean Entering 'ome-model' HEAD detached from 3d70a1f9 nothing to commit, working tree clean Entering 'ome-poi' HEAD detached from da3a5f3 nothing to commit, working tree clean Entering 'ome-stubs' HEAD detached from 1559997 nothing to commit, working tree clean + echo 'Push all branches' Push all branches ++ git config github.user + user=snoopycrimecop + git submodule foreach 'git push -f git@github.com:snoopycrimecop/${path}.git HEAD:merge_ci' Entering 'ZarrReader' Everything up-to-date Entering 'bio-formats-documentation' Everything up-to-date Entering 'bio-formats-examples' Everything up-to-date Entering 'bioformats' Everything up-to-date Entering 'ome-codecs' Everything up-to-date Entering 'ome-common-java' Everything up-to-date Entering 'ome-jai' Everything up-to-date Entering 'ome-mdbtools' Everything up-to-date Entering 'ome-metakit' Everything up-to-date Entering 'ome-model' Everything up-to-date Entering 'ome-poi' Everything up-to-date Entering 'ome-stubs' Everything up-to-date + echo 'Commit all component version changes' Commit all component version changes + git add -u + git commit -m 'Update component versions' HEAD detached from 5113234 nothing to commit, working tree clean + true + git push -f git@github.com:snoopycrimecop/bio-formats-build.git HEAD:merge_ci Everything up-to-date [BIOFORMATS-push] $ /bin/bash -xe /tmp/jenkins18094178090446566028.sh + mkdir -p /home/omero/workspace/BIOFORMATS-push/target + cd /home/omero/workspace/BIOFORMATS-push/target + curl -sfL https://github.com/ome/build-infra/archive/master.tar.gz + tar -zxf - + export PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/omero/workspace/BIOFORMATS-push/target/build-infra-master/ + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/omero/workspace/BIOFORMATS-push/target/build-infra-master/ + cd /home/omero/workspace/BIOFORMATS-push/bio-formats-build + foreach-get-version + foreach-get-version-as-property + sed -i s/9.0.0-SNAPSHOT/8.5.0/ /home/omero/workspace/BIOFORMATS-push/target/version.properties + sed -i s/9.0.0-SNAPSHOT/8.5.0/ /home/omero/workspace/BIOFORMATS-push/target/version.tsv Archiving artifacts Finished: SUCCESS